Of course, there were a few issues I had to fix in order to get the test site to function properly - changing the config.php and .htaccess files and the forum url in the AdminCP for example. When I was done I was able to access both sites and both forums functioned properly and independently.
Then I went to upgrade the test site to XF 1.2 - uploaded the files to adminextra.org, ran the install script - everything went as it should - no problems at all. Except...
... for some inexplicable reason, adminextra.com started upgrading as well - which was completely unwanted behavior not to mention the fact that I hadn't uploaded the XF 1.2 files to adminextra.com. The forum running on adminextra.com (yeah, the live site) didn't auto-close - just looked wonky and had an upgrading notice showing. Then it got stuck. I went to the AdminCP - even wonkier looking, but there was something there telling me to complete the upgrade so I pushed the button - taken to the install/upgrade script but was told that I was already running 1.1.5 so no upgrade available (since I hadn't uploaded the 1.2 files). So, I then uploaded the 1.2 files to adminextra.com and ran the install/upgrade script again. I was surprised that it ran, but it wasn't normal - I had to manually hit the continue button every time it stopped. It did run through to the end though, and for the most part everything was OK.
Except of course for 2 things - now I have to scramble to make everything work on a live site with a custom skin and multiple addons after an unplanned (accidental even) upgrade - but at least the site is up and running. But more important - I have no idea why running the upgrade on adminextra.org triggered the upgrade on adminextra.com. I spoke with my host at length and they did a bunch of investigating - they say the two sites appear to be completely separate and see no reason for the cross site scripting or whatever you call it and blame it on the XenForo install script. They need to know if there's anything in the script that could cause this. In the meantime, they're gonna monitor both sites when I do the next upgrade to adminextra.org to see if/how it affects adminextra.com.
So, any ideas?